13-89990531-C-T

Variant names:

• chr13-89990531-C-T
• rs6492466

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.271 in 151,846 control chromosomes in the GnomAD database, including 5,768 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (5768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41159 AN: 151728 Hom.: 5768 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.271 AC: 41179 AN: 151846 Hom.: 5768 Cov.: 31 AF XY: 0.269 AC XY: 19993 AN XY: 74194

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.281

Alfa AF: 0.289 Hom.: 13200

Bravo AF: 0.262

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.1
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6492466; hg19: chr13-90642785;